LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 30.843872601504287*${_u_distance} variable xmax_converted equal 30.843872601504287*1 variable ymin_converted equal -61.69179520189546*${_u_distance} variable ymin_converted equal -61.69179520189546*1 variable ymax_converted equal 61.69179520189546*${_u_distance} variable ymax_converted equal 61.69179520189546*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 Lattice spacing in x,y,z = 4.05 4.05 4.05 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 61.6917952018955 ${zmin_converted} ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 61.6917952018955 0 ${zmax_converted} units box region whole block 0 30.8438726015043 -61.6917952018955 61.6917952018955 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -61.6918 0) to (30.8439 61.6918 4.05) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 61.6917952018955 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31791 5.31791 4.05 create_atoms 1 region upper Created 466 atoms create_atoms CPU = 0.000215054 secs group upper type 1 466 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.4270978976387587 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.6917952018955 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31791 5.31791 4.05 create_atoms 2 region lower Created 466 atoms create_atoms CPU = 9.39369e-05 secs group lower type 2 466 atoms in group lower displace_atoms lower move -3.4270978976387587 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_721930391003_000-files/b'AlU-library.meam' Al U ./SM_721930391003_000-files/b'AlU.meam' Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 16 atoms, new total = 916 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3051.6708 0 -3051.6708 2334.4947 334 0 -3066.7198 0 -3066.7198 -3795.2368 Loop time of 6.17063 on 1 procs for 334 steps with 916 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3051.67076424 -3066.71984439 -3066.71984439 Force two-norm initial, final = 23.5602 9.35885e-06 Force max component initial, final = 6.90135 1.54508e-06 Final line search alpha, max atom move = 1 1.54508e-06 Iterations, force evaluations = 334 662 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1309 | 6.1309 | 6.1309 | 0.0 | 99.36 Neigh | 0.002496 | 0.002496 | 0.002496 | 0.0 | 0.04 Comm | 0.0223 | 0.0223 | 0.0223 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01498 | | | 0.24 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5707 ave 5707 max 5707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35890 ave 35890 max 35890 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71780 ave 71780 max 71780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71780 Ave neighs/atom = 78.3624 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes Step Temp E_pair E_mol TotEng Press Volume 334 0 -3066.7198 0 -3066.7198 -3795.2368 15412.788 1334 0 -3066.7955 0 -3066.7955 -654.72512 15348.024 Loop time of 18.7713 on 1 procs for 1000 steps with 916 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3066.71984439 -3066.79548189 -3066.79548198 Force two-norm initial, final = 48.6294 0.023804 Force max component initial, final = 37.8639 0.0224457 Final line search alpha, max atom move = 0.311381 0.00698915 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.498 | 18.498 | 18.498 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.060216 | 0.060216 | 0.060216 | 0.0 | 0.32 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2126 | | | 1.13 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5592 ave 5592 max 5592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36106 ave 36106 max 36106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72212 ave 72212 max 72212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72212 Ave neighs/atom = 78.8341 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.0 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.79 | 10.79 | 10.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3066.7955 0 -3066.7955 -654.72512 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5639 ave 5639 max 5639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36816 ave 36816 max 36816 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73632 ave 73632 max 73632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73632 Ave neighs/atom = 80.3843 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 10.79 | 10.79 | 10.79 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3066.7955 -3066.7955 30.80759 123.38359 4.0377306 -654.72512 -654.72512 -0.34642413 -1961.4929 -2.3359994 2.5175325 530.70924 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5639 ave 5639 max 5639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36816 ave 36816 max 36816 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73632 ave 73632 max 73632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73632 Ave neighs/atom = 80.3843 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_046.3972/numatoms.out 916 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3066.79548197731-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3066.79548197731-916*${isolated_atom_energy} variable adjusted_pe_metal equal -3066.79548197731-916*0 print "${adjusted_pe_metal} eV" file output/dump_046.3972/energy.out -3066.79548197731 eV print "${mindist_metal} Angstroms" file output/dump_046.3972/mindistance.out 2.51753252564592 Angstroms write_dump all cfg output/dump_046.3972/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_046.3972/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:24